Two sequence classes of kinetoplastid 5S ribosomal RNA gene revealed among bodonid spliced leader RNA gene arrays

Sant’Ana, Débora de Mello Gonçales

doi:10.1016/s0378-1097(01)00405-0

Cited by 7 publications

(7 citation statements)

References 12 publications

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“…Thirty-four sequenced DNA fragments were SL RNA gene-specific : they contained recognizable SL RNA features including the conserved exon and intron followed by a T-tract and a variable intergenic region. In several cases, the intergenic region of the SL RNA gene repeat contained the 5S rRNA gene, which is linked with SL RNA genes in some trypanosomatids and bodonids (Santana et al 2001). Several cloned and sequenced bands (42B, 44B, 47B, 48B, 50B, 52B, 55B) were dimers, some of which (47B, 48B, 50B, and 52B) differed internally by a single nucleotide in the intergenic region, as seen previously (Dollet et al 2001).…”

Section: R E S U L T S a N D Discussionsupporting

confidence: 58%

Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene

et al. 2004

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The biodiversity of insect trypanosomes is largely unknown, resulting in significant gaps in the understanding of pathogen evolution. A culture-independent preliminary survey of trypanosomatid fauna was conducted for the parasites of Heteroptera (Hemiptera) from several localities in Costa Rica. Trypanosomatid infections were detected by light microscopy of smeared gut contents. Out of 257 insects representing 6 families, infections were found in 62 cases; cultures were obtained for 29 new isolates. Gut material from infected hosts was preserved in the field using an SDS-EDTA buffer solution for subsequent DNA extraction in the laboratory. PCR amplification of the trypanosomatid-specific spliced leader (SL) RNA gene repeats was successful for 60 field samples. Eighteen distinct SL RNA typing units were identified in a set of 28 samples analysed in detail. Cluster analysis indicated that these typing units were unique and thus could represent new species and, in some cases, new genera. This study reveals only a minor fraction of the trypanosomatid biodiversity, which is anticipated to be high.

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Section: R E S U L T S a N D Discussionsupporting

confidence: 58%

Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene

et al. 2004

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“…Speculating on the arrangement of nucleosomes in the 1.4-kb T. brucei SL RNA gene array, which encodes a ~150-nt primary transcript and has the largest non-transcribed intergenic region characterized among the kinetoplastids, we would envisage 220-bp nucleosome-free regions spanning the promoter element and transcribed regions separated by up to five bound nucleosomes. Likewise, SL RNA gene arrays that are interspersed with 5S rRNA genes [52] may limit nucleosome binding to the non-transcribed regions, space permitting. The length of the MINA array is just sufficient to accommodate a single nucleosome, a fortuitous situation for our nucleosome mapping.…”

Section: Discussionmentioning

confidence: 99%

The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes

et al. 2007

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BackgroundThe spliced leader (SL) RNA provides the 5' m7G cap and first 39 nt for all nuclear mRNAs in kinetoplastids. This small nuclear RNA is transcribed by RNA polymerase II from individual promoters. In Leishmania tarentolae the SL RNA genes reside in two multi-copy tandem arrays designated MINA and MINB. The transcript accumulation from the SL promoter on the drug-selected, episomal SL RNA gene cassette pX-tSL is ~10% that of the genomic array in uncloned L. tarentolae transfectants. This disparity is neither sequence- nor copy-number related, and thus may be due to interference of SL promoter function by epigenetic factors. To explore these possibilities we examined the nucleoplasmic localization of the SL RNA genes as well as their nucleosomal architecture.ResultsThe genomic SL RNA genes and the episome did not co-localize within the nucleus. Each genomic repeat contains one nucleosome regularly positioned within the non-transcribed intergenic region. The 363-bp MINA array was resistant to micrococcal nuclease digestion between the -258 and -72 positions relative to the transcription start point due to nucleosome association, leaving the promoter elements and the entire transcribed region exposed for protein interactions. A pattern of ~164-bp protected segments was observed, corresponding to the amount of DNA typically bound by a nucleosome. By contrast, nucleosomes on the pX-tSL episome were randomly distributed over the episomal SL cassette, reducing transcription factor access to the episomal promoter by approximately 74%. Cloning of the episome transfectants revealed a range of transcriptional activities, implicating a mechanism of epigenetic heredity.ConclusionThe disorganized nucleosomes on the pX episome are in a permissive conformation for transcription of the SL RNA cassette approximately 25% of the time within a given parasite. Nucleosome interference is likely the major factor in the apparent transcriptional repression of the SL RNA gene cassette. Coupled with the requirement for run-around transcription that drives expression of the selectable drug marker, transcription of the episomal SL may be reduced even further due to sub-optimal nucleoplasmic localization and initiation complex disruption.

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“…After trans‐splicing was discovered in Euglena (Muchal and Scwartzbach 1992), Cavalier‐Smith (1993b) postulated that trans‐splicing of all protein‐coding genes originated in the ancestral euglenozoan and would be found in all euglenozoan groups, proposing universal trans‐splicing as a unique molecular synapomorphy for Euglenozoa (Cavalier‐Smith 1993b, 1995). Subsequently trans‐splicing was found in diplonemids (Sturm et al 2001), bodonids (Santana et al 2001) and prokinetoplastids (Dykova et al 2003). It is now known in many euglenoids, but although all genes examined in most genera are trans‐spliced, the three studied to date in Dis‐rigma proteus are not, though traces of mini‐exons were found (Frantz et al 2000).…”

Section: Discussionmentioning

confidence: 99%

Ribosomal RNA Phylogeny of Bodonid and Diplonemid Flagellates and the Evolution of Euglenozoa

Heyden

Chao

Vickerman

2004

J Eukaryotic Microbiology

121

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Euglenozoa is a major phylum of excavate protozoa (comprising euglenoids, kinetoplastids, and diplonemids) with highly unusual nuclear, mitochondrial, and chloroplast genomes. To improve understanding of euglenozoan evolution, we sequenced nuclear small-subunit rRNA genes from 34 bodonids (Bodo, Neobodo, Parabodo, Dimastigella-like, Rhynchobodo, Rhynchomonas, and unidentified strains), nine diplonemids (Diplonema, Rhynchopus), and a euglenoid (Entosiphon). Phylogenetic analysis reveals that diplonemids and bodonids are more diverse than previously recognised, but does not clearly establish the branching order of kinetoplastids, euglenoids, and diplonemids. Rhynchopus is holophyletic; parasitic species arose from within free-living species. Kinetoplastea (bodonids and trypanosomatids) are robustly holophyletic and comprise a major clade including all trypanosomatids and most bodonids ('core bodonids') and a very divergent minor one including Ichthyobodo. The root of the major kinetoplastid clade is probably between trypanosomatids and core bodonids. Core bodonids have three distinct subclades. Clade 1 has two distinct Rhynchobodo-like lineages; a lineage comprising Dimastigella and Rhynchomonas; and another including Cruzella and Neobodo. Clade 2 comprises Cryptobia/ Trypanoplasma, Procryptobia, and Parabodo. Clade 3 is an extensive Bodo saltans species complex. Neobodo designis is a vast genetically divergent species complex with mutually exclusive marine and freshwater subclades. Our analysis supports three phagotrophic euglenoid orders: Petalomonadida (holophyletic), Ploeotiida (probably holophyletic), Peranemida (paraphyletic).

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Two sequence classes of kinetoplastid 5S ribosomal RNA gene revealed among bodonid spliced leader RNA gene arrays

Cited by 7 publications

References 12 publications

Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene

Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene

The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes

Ribosomal RNA Phylogeny of Bodonid and Diplonemid Flagellates and the Evolution of Euglenozoa

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